SeqBench

Multiple Sequence Alignment (MSA) Viewer

Align several DNA or protein sequences and view a colored alignment with a consensus.

🔒 Inputs are not logged; MAFFT/MUSCLE temporary files are deleted after the run

Paste sequences in FASTA, choose local center-star or server MAFFT/MUSCLE, and run a multiple sequence alignment. Browse the colored residues, consensus and conservation in pages; download the full aligned FASTA or export the visible region as SVG/PNG. Local center-star works offline; MAFFT and MUSCLE support up to 200 sequences and send the input to SeqBench for computation.

0 sequence(s)

Run alignment sends your sequences to SeqBench's server. Temporary alignment files are deleted when the run finishes. No external alignment service receives them. Up to 200 sequences, 10,000 residues each, 100,000 total; 60-second runtime limit.

MAFFT selects a strategy for your data; MUSCLE uses its PPP algorithm. Neither silently falls back to center-star. Check ambiguous protein sequences with an explicit sequence type. Conservation and the consensus use all rows, including rows outside the current page. Up to 4,000,000 alignment cells can be returned.

How to use the MSA Viewer tool

  1. 1Paste two or more sequences in FASTA format (or load the example).
  2. 2Choose DNA/RNA or protein and an alignment method, then click Align. Browse the alignment, consensus and conservation.
  3. 3Export the figure as SVG/PNG, download the alignment as FASTA, or share the link.

Frequently asked questions

How does the alignment work?

Choose local center-star for up to 25 short sequences, or MAFFT/MUSCLE for up to 200 sequences, 10,000 residues per sequence and 100,000 input residues total. Native runs use temporary files on SeqBench servers; the files are deleted after completion, failure or cancellation. Inputs are not sent to an upstream alignment service.

Can I align protein sequences too?

Yes. The viewer detects whether your sequences are nucleotide or protein and colors them accordingly (nucleotide palette, or a Clustal-style amino-acid grouping).

Can I export the alignment figure?

Yes — export the visible alignment region as a vector SVG or a high-resolution PNG, or download all aligned sequences as FASTA.

More

Guides

Related tools

Variant Comparator

Align a query to a reference and list substitutions, insertions and deletions with effects.

Pairwise Alignment

Align two sequences with Needleman-Wunsch or Smith-Waterman.

HGVS Converter

Convert an HGVS c. variant to genomic (g.) coordinates and predict its protein (p.) effect, via a real, live Ensembl exon map.